Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate Echvi_3019 Echvi_3019 Glucose/sorbosone dehydrogenases
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__Cola:Echvi_3019 Length = 387 Score = 182 bits (461), Expect = 2e-50 Identities = 114/332 (34%), Positives = 166/332 (50%), Gaps = 35/332 (10%) Query: 24 EEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFREGRLSTYAELP-VYHRGESGLLGLAL 82 E +V + PW +A LPDGG+L+ E+ G + ++G P V +G+ GLL + L Sbjct: 52 ETIVEDINNPWGMALLPDGGILVTEKAGELIYAKDGEKKIIPGTPDVVSKGQGGLLDIIL 111 Query: 83 HPRFPEAPYVYAYRTVAEG---GLRNQVVRLRHLGERGVLDRVVLDGIPARPHGLHSGGR 139 HP + ++Y + EG G V+R + G V+ P G H G R Sbjct: 112 HPDYATNGWIYFTYSSGEGEEDGAHTAVMRAKFHGNSLTDQEVLYKATPNTDKGQHFGSR 171 Query: 140 IAFGPDGMLYVTTGEVYEREL-AQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPEVYS 198 +AF +G LY + GE ER++ QD+ GGKI R+ +G NPF A+ ++S Sbjct: 172 MAFDEEGYLYFSIGERGERDVNPQDITRDGGKIYRIHDDGSIPNDNPFFNEEDAKKAIFS 231 Query: 199 LGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRVVGRG------ 252 GHRNPQG+ +HP E++ +EHGP G DE+N++ GGN+GWP VV G Sbjct: 232 YGHRNPQGMIFHPVYNEIWVNEHGPQ-----GGDEINIVEKGGNFGWP-VVSYGINYDDS 285 Query: 253 ------NDPRYRDPLYFW-----PQGF---PPGNLAFFRGDLYVAGLRGQALLRLVLEGE 298 + PLY+W P GF P + G+L V L+ Q L L L+G+ Sbjct: 286 ILTEETSKEGMEQPLYYWVPSIAPCGFALVPEETYPQWAGNLLVGSLKFQYLEMLSLDGK 345 Query: 299 RGRWRVLRVETALSGFGRLREVQVGPDGALYV 330 +V + + G GRLR V++GPD +YV Sbjct: 346 ----QVTKRTKLMDGAGRLRNVKIGPDNHIYV 373 Lambda K H 0.322 0.146 0.460 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 498 Number of extensions: 37 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 352 Length of database: 387 Length adjustment: 30 Effective length of query: 322 Effective length of database: 357 Effective search space: 114954 Effective search space used: 114954 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory